Contacts of the helix formed by residues 3 - 21 (chain A) in PDB entry 4ETO
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with CYS 3 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2A ALA* 1.3 78.9 - - - +
4A PRO* 1.3 67.4 - - - +
5A LEU 3.2 2.2 - - - -
6A GLU* 2.9 26.4 + - + +
7A LYS* 3.1 16.6 + - - +
40B ARG 3.7 11.9 - - - -
41B GLU* 3.8 16.4 - - - +
43B PRO* 3.5 36.6 - - - -
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Residues in contact with PRO 4 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2A ALA* 3.4 18.6 - - + +
3A CYS* 1.3 82.0 - - - +
5A LEU* 1.3 57.4 + - - +
7A LYS* 3.2 14.5 + - + +
8A ALA* 2.8 27.7 + - - +
11B VAL* 3.7 25.4 - - + +
15B THR* 5.3 1.6 - - - +
41B GLU* 4.3 12.1 - - - +
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Residues in contact with LEU 5 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3A CYS 3.2 1.0 - - - -
4A PRO* 1.3 79.7 - - - +
6A GLU* 1.3 59.0 + - - +
8A ALA* 3.3 3.9 + - + +
9A LEU* 3.0 31.2 + - + +
11B VAL* 3.8 10.2 - - + +
12B MET* 4.1 20.2 - - + -
15B THR* 4.0 21.3 + - + +
37B LEU* 4.2 11.4 - - + -
41B GLU* 4.0 20.4 + - + +
42B LEU* 4.0 25.6 - - + -
75B TYR* 3.7 25.6 - - - +
79B LEU* 4.0 24.9 - - + -
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Residues in contact with GLU 6 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3A CYS* 2.9 19.3 + - + +
5A LEU* 1.3 74.4 - - - +
7A LYS* 1.3 66.6 + - + +
9A LEU* 3.4 9.0 + - - +
10A ASP* 3.1 21.8 + - - +
41B GLU 3.5 13.5 - - - +
42B LEU* 3.1 18.4 - - + -
43B PRO* 3.2 8.6 - - - +
44B SER* 2.5 54.1 + - - -
45B PHE* 3.6 18.8 - - + -
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Residues in contact with LYS 7 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2A ALA* 4.1 26.2 - - - +
3A CYS 3.1 15.6 + - - +
4A PRO* 3.2 15.1 + - + +
6A GLU* 1.3 78.3 - - + +
8A ALA* 1.3 60.8 + - - +
10A ASP* 3.2 7.4 + - - +
11A VAL* 3.1 28.5 + - + +
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Residues in contact with ALA 8 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4A PRO 2.8 13.4 + - - +
5A LEU* 3.5 19.1 - - + +
6A GLU 3.2 0.4 - - - -
7A LYS* 1.3 72.0 - - - +
9A LEU* 1.3 68.2 + - - +
11A VAL* 3.2 5.1 + - - +
12A MET* 2.9 32.4 + - - +
8B ALA* 3.7 38.9 - - + +
11B VAL* 4.3 7.2 - - + -
12B MET* 4.8 0.4 - - + -
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Residues in contact with LEU 9 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5A LEU* 3.0 17.6 + - + +
6A GLU* 3.7 5.4 - - - +
7A LYS 3.3 0.2 - - - -
8A ALA* 1.3 78.3 - - + +
10A ASP* 1.4 62.1 + - - +
12A MET* 3.3 23.9 + - + +
13A VAL* 3.1 26.3 + - + +
42B LEU* 3.6 31.6 - - + -
45B PHE* 4.0 13.7 - - + -
79B LEU* 3.5 39.5 - - + +
82B ILE* 3.8 21.8 - - + -
83B ALA* 4.1 14.4 - - + +
86B CYS* 6.0 2.7 - - - -
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Residues in contact with ASP 10 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6A GLU 3.1 13.7 + - - +
7A LYS* 3.2 10.7 + - - +
9A LEU* 1.4 75.8 - - - +
11A VAL* 1.3 60.5 + - - +
13A VAL* 3.4 6.5 + - - +
14A SER* 2.8 39.1 + - - -
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Residues in contact with VAL 11 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7A LYS* 3.1 15.9 + - + +
8A ALA* 3.6 7.6 - - - +
10A ASP* 1.3 77.2 - - - +
12A MET* 1.3 64.9 + - - +
14A SER* 3.7 7.6 - - - +
15A THR* 2.6 42.4 + - - +
4B PRO* 3.7 43.1 - - + +
5B LEU* 3.7 10.3 - - + +
8B ALA* 4.2 4.5 - - + -
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Residues in contact with MET 12 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8A ALA* 2.9 24.2 + - - +
9A LEU* 3.5 28.0 - - + +
11A VAL* 1.3 75.1 - - - +
13A VAL* 1.3 62.2 + - - +
16A PHE 3.7 1.6 + - - -
72A PHE* 4.6 0.9 - - - -
75A TYR* 2.7 36.0 + - + -
76A CYS* 5.4 5.6 - - + -
79A LEU* 4.1 20.4 - - + -
5B LEU* 3.9 15.5 - - + -
8B ALA* 4.4 4.9 - - + -
9B LEU* 6.0 1.3 - - + -
12B MET* 3.9 35.0 - - + +
79B LEU* 5.0 6.1 - - + +
80B SER* 5.5 3.1 - - - +
83B ALA* 4.2 15.5 - - + -
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Residues in contact with VAL 13 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9A LEU 3.1 14.7 + - - +
10A ASP* 3.8 7.6 - - - +
12A MET* 1.3 76.2 - - - +
14A SER* 1.3 65.0 + - - +
15A THR 3.3 0.5 + - - -
16A PHE* 3.4 8.0 + - - +
17A HIS* 3.3 22.6 - - + -
72A PHE* 3.8 12.6 - - + -
83B ALA* 3.7 30.7 - - + +
86B CYS* 4.5 12.3 - - + -
87B ASN* 4.0 26.0 - - - +
90B PHE* 4.3 17.3 - - + -
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Residues in contact with SER 14 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10A ASP* 2.8 32.0 + - - -
11A VAL* 3.6 9.5 + - - +
13A VAL* 1.3 77.5 - - - +
15A THR* 1.3 66.1 + - - +
17A HIS* 3.2 4.9 + - - +
18A LYS* 3.1 20.6 + - - +
90B PHE* 4.9 15.3 - - - -
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Residues in contact with THR 15 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11A VAL* 2.6 37.9 + - - +
13A VAL 3.2 0.2 - - - -
14A SER* 1.3 81.6 + - - +
16A PHE* 1.3 63.9 + - - +
18A LYS* 3.3 15.9 + - + +
19A TYR* 3.3 15.0 - - + -
37A LEU* 3.8 6.5 - - + +
41A GLU* 3.6 39.3 + - + +
75A TYR* 3.8 8.1 - - - +
4B PRO* 5.4 1.2 - - - +
5B LEU* 4.0 19.3 - - + +
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Residues in contact with PHE 16 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13A VAL 3.4 9.8 + - - +
14A SER 3.3 0.2 - - - -
15A THR* 1.3 77.2 - - - +
17A HIS* 1.3 78.2 + + - +
19A TYR* 3.1 8.0 + - - +
20A SER* 3.0 42.0 + - - -
27A PHE 3.2 31.0 - - - -
28A LYS* 4.0 2.2 - - - -
29A LEU* 3.6 27.9 - - + +
37A LEU* 4.1 8.5 - - - -
70A VAL 3.6 14.1 - - - -
71A ASP 3.7 13.0 - - - -
72A PHE* 3.6 27.1 - + + -
75A TYR* 3.6 40.1 + + + -
91B GLU* 5.1 0.2 - - - -
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Residues in contact with HIS 17 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13A VAL* 3.3 23.1 - - + -
14A SER 3.2 6.9 + - - +
16A PHE* 1.3 91.3 - + - +
18A LYS* 1.3 64.5 + - - +
19A TYR 3.1 2.7 + - - -
20A SER* 3.6 15.2 + - - -
21A GLY* 4.0 9.2 + - - -
26A LYS 4.3 1.0 + - - -
27A PHE* 3.8 20.3 - + - -
72A PHE* 4.6 0.4 - + - -
87B ASN* 2.7 29.0 + - - -
90B PHE* 3.5 45.8 - + + -
91B GLU* 3.8 20.2 - - + -
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Residues in contact with LYS 18 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14A SER 3.1 10.6 + - - +
15A THR* 3.4 17.5 - - + +
17A HIS* 1.3 78.7 - - - +
19A TYR* 1.3 72.4 + - + +
21A GLY* 5.1 0.4 - - - -
22A LYS* 3.7 16.3 - - - +
41A GLU* 2.9 30.9 + - - +
4B PRO* 6.3 1.0 - - - +
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Residues in contact with TYR 19 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15A THR 3.3 15.9 - - - -
16A PHE 3.1 2.6 + - - +
18A LYS* 1.3 101.9 - - + +
20A SER* 1.3 64.9 + - - +
21A GLY 3.1 4.4 + - - -
22A LYS* 3.5 17.1 - - - +
29A LEU* 3.7 18.6 - - + -
33A GLU* 3.2 27.9 - - + +
36A GLU* 3.7 41.7 - - + -
37A LEU* 3.7 20.0 - - + -
40A ARG* 3.4 30.0 + - - +
41A GLU* 2.7 41.9 + - + -
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Residues in contact with SER 20 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16A PHE* 3.0 42.3 + - - -
17A HIS* 3.6 11.8 + - - -
18A LYS 3.9 0.2 - - - -
19A TYR* 1.3 77.1 - - - +
21A GLY* 1.3 57.7 + - - +
22A LYS 3.4 0.4 - - - -
25A ASP 3.1 8.7 - - - +
26A LYS* 2.9 17.5 + - - +
28A LYS 3.6 19.1 - - - -
29A LEU* 3.7 8.5 - - - +
33A GLU* 3.1 1.0 - - - +
101A CA 2.4 25.4 - - - -
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Residues in contact with GLY 21 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17A HIS 4.0 8.8 + - - -
18A LYS 5.1 0.2 - - - -
19A TYR 3.1 1.8 - - - -
20A SER* 1.3 80.9 + - - +
22A LYS* 1.3 62.5 + - - +
23A GLU 3.5 1.1 + - - -
26A LYS* 3.9 41.6 - - - +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il